BME100 f2014:Group16 L4

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BME 100 Fall 2014 Home
Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
Course Logistics For Instructors
Wiki Editing Help


Name: Gurpaul Sidhu
Role(s): Wiki editor, researcher
Picture Source:www.
Name: Christopher Saar
Protocol editer
Name: Emily Angeles Mancinas
Name: Leslie Bernardino
Role(s): observer
Name: Sheania Morgan
Conductor of experiment
Name: Romann Arizmendi




  • Lab Coat
  • Disposable gloves
  • PCR reaction mix - containts Taq DNA polymerase, MgCl2, and dNTP's - 8 tubes - 50 microliters each
  • DNA/primer mix - each mix contains different template DNA - 8 tubes - 50 microliters each
  • strip of empty PCR tubes
  • disposable pipette tips
  • cup for discarded tips
  • micropipettor
  • OpenPCR machine

PCR Reaction Sample List

Tube Label PCR Reaction Sample Patient ID
G16 + Positive control none
G16 - Negative control none
G16 1-1 Patient 1, replicate 1 37465
G16 1-2 Patient 1, replicate 2 37465
G16 1-3 Patient 1, replicate 3 37465
G16 2-1 Patient 2, replicate 1 28404
G16 2-2 Patient 2, replicate 2 28404
G16 2-3 Patient 2, replicate 3 28404

DNA Sample Set-up Procedure

  • Step 1 Set the micro pipette to 50 micro-liter
  • Step 2 Attach a fresh micro pipette tube to the micro pipette pump.
  • Step 3 Draw Patient DNA of 50 micro-liters
  • Step 4 Deposit Patient DNA into empty PCR container
  • Step 5 Dispose of micro pipette tip
  • Step 6 Attach a fresh micro pipette tube to the micro pipette pump.
  • Step 7 Draw PCR of 50 micro-liters
  • Step 8 Deposit PCR of 50 micro-liters into empty PCR container
  • Step 9 Dispose of micro pipette tip
  • Step 10 Placing the tubes in the Thermal Cycler
  • Step 11 Repeat steps 1-10

OpenPCR program
For the PCR setting, the heated lid was set to 100 degrees Celsius, then the initial step was set for 95 degrees Celsius for 2 minutes. 22 cycles were preformed, the samples were denatured at 95 degrees for 30 seconds, Anneal at 57 degrees for 30 seconds, and the extended at 72 degrees for 30 seconds as well. for the final step the temperature was set to 72 degrees Celsius for 2 minutes, and finally set final hold to 4 degrees Celsius.

Research and Development

PCR - The Underlying Technology

Components of a PCR
There are four main components of a PCR: template DNA, primers, taq Polymerase, and Deoxyribonucleotides The DNA template is the section of the entire strand that contains the target sequence desired in the study. Within the reaction, heating the DNA to 95 degrees Celsius, allows it to separate so that the template can be isolated. Secondly, primers are combinations of nucleotides that are complementary to the target sequence of DNA. This allows for duplicate strands to be instantiated without superfluous DNA. Taq Polymerase, is able to synthesize the replicate strands that are complimentary to the target strand. Taq Polymerase is utilized for two reasons: the first being that it is heat resistance which is important when temperatures are constantly changing and the second being that it only requires the template and two primers to create duplicate segments. Finally, dNTPs are the individual bases - adenine, guanine, thymine, and cytosine - that are employed by the polymerase in order to create the new strands of DNA during the reaction.

Phases of a PCR
The first phase of a PCR requires raising the temperature of the DNA strand to 95 degrees Celsius so that the hydrogen bonds can begin to break. The second step, holds the chamber at 95 degrees so that the DNA template can be completely separated into two strands. The temperature is subsequently lowered to 57 degrees which begins the process of introducing primers into the substance. The primers are able to bond to the complementary bases present on the template strand at this temperature. Afterwards, the temperature is one again increase to 72 degrees Celsius so that the Taq polymerase can match the bases on the template strand with the nucleotides that exist in the solution to create new strands. The final step holds the temperature constant for three minutes to ensure that the template DNA is fully extended. The final hold brings the temperature down so that the hydrogen bonds in the new DNA strands are strengthened, thus replicating the target DNA successfully.

Bases that are Paired Together During a PCR
In order to ensure that DNA replication results in the same sequencing of bases, each base is paired with a complementary base. Adenine is paired with Thymine and Cytosine is paired with Guanine.

Base-Pairing During Thermal Cycling
The two steps that incorporate the process of base pairing are annealing and extension steps. The annealing step begins the pairing when the primer attaches to the template DNA strand. The extension step involves the Taq polymerase which takes free nucelotides and binds them to their complementary bases.